2023
The functional and evolutionary impacts of human-specific deletions in conserved elements
Xue J, Mackay-Smith A, Mouri K, Garcia M, Dong M, Akers J, Noble M, Li X, Lindblad-Toh K, Karlsson E, Noonan J, Capellini T, Brennand K, Tewhey R, Sabeti P, Reilly S, Andrews G, Armstrong J, Bianchi M, Birren B, Bredemeyer K, Breit A, Christmas M, Clawson H, Damas J, Di Palma F, Diekhans M, Dong M, Eizirik E, Fan K, Fanter C, Foley N, Forsberg-Nilsson K, Garcia C, Gatesy J, Gazal S, Genereux D, Goodman L, Grimshaw J, Halsey M, Harris A, Hickey G, Hiller M, Hindle A, Hubley R, Hughes G, Johnson J, Juan D, Kaplow I, Karlsson E, Keough K, Kirilenko B, Koepfli K, Korstian J, Kowalczyk A, Kozyrev S, Lawler A, Lawless C, Lehmann T, Levesque D, Lewin H, Li X, Lind A, Lindblad-Toh K, Mackay-Smith A, Marinescu V, Marques-Bonet T, Mason V, Meadows J, Meyer W, Moore J, Moreira L, Moreno-Santillan D, Morrill K, Muntané G, Murphy W, Navarro A, Nweeia M, Ortmann S, Osmanski A, Paten B, Paulat N, Pfenning A, Phan B, Pollard K, Pratt H, Ray D, Reilly S, Rosen J, Ruf I, Ryan L, Ryder O, Sabeti P, Schäffer D, Serres A, Shapiro B, Smit A, Springer M, Srinivasan C, Steiner C, Storer J, Sullivan K, Sullivan P, Sundström E, Supple M, Swofford R, Talbot J, Teeling E, Turner-Maier J, Valenzuela A, Wagner F, Wallerman O, Wang C, Wang J, Weng Z, Wilder A, Wirthlin M, Xue J, Zhang X. The functional and evolutionary impacts of human-specific deletions in conserved elements. Science 2023, 380: eabn2253. PMID: 37104592, PMCID: PMC10202372, DOI: 10.1126/science.abn2253.Peer-Reviewed Original ResearchConceptsHuman-specific deletionHuman phenotypic traitsParallel reporterEvolutionary impactDevelopmental genesPhenotypic traitsEvolutionary mechanismsGenomic sequencesNew traitsTranscriptomic datasetsSequence altersRegulatory functionsCell typesRegulatory activityRich resourceDeletionSynaptic functionTraitsBrain developmentGenesSpeciesReporterHumansSequenceExpression
2017
Cerebral organoids reveal early cortical maldevelopment in schizophrenia—computational anatomy and genomics, role of FGFR1
Stachowiak E, Benson C, Narla S, Dimitri A, Chuye L, Dhiman S, Harikrishnan K, Elahi S, Freedman D, Brennand K, Sarder P, Stachowiak M. Cerebral organoids reveal early cortical maldevelopment in schizophrenia—computational anatomy and genomics, role of FGFR1. Translational Psychiatry 2017, 7: 6. PMID: 30446636, PMCID: PMC5802550, DOI: 10.1038/s41398-017-0054-x.Peer-Reviewed Original ResearchConceptsNeural progenitor cellsCerebral organoidsSchizophrenia patientsVentricular zoneInduced pluripotent stem cellsCortical neuronal maturationUtero brain developmentRole of FGFR1Stem cellsIntracortical connectivityFirst trimesterCortical maldevelopmentCortical malformationsPreventive treatmentCalretinin interneuronsNeuronal maturationSubcortical regionsControl individualsPioneer neuronsCortical zoneBrain developmentHuman embryonic stem cellsProgenitor cellsIntegrative nuclear FGFR1FGFR1 geneApplication of CRISPR/Cas9 to the study of brain development and neuropsychiatric disease
Powell S, Gregory J, Akbarian S, Brennand K. Application of CRISPR/Cas9 to the study of brain development and neuropsychiatric disease. Molecular And Cellular Neuroscience 2017, 82: 157-166. PMID: 28549865, PMCID: PMC5516945, DOI: 10.1016/j.mcn.2017.05.007.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsCRISPR/Cas9 technologyPluripotent stem cellsTranscriptional regulatorsManipulation of DNAEpigenetic pathwaysGenomic editingSpecific lociCRISPR/Basic biologyCas9 technologyGene expressionStem cellsTargeted localizationEnzyme activityBrain developmentEpigenomeNeuropsychiatric diseasesGenomeCRISPRRepressionLociBiologyRegulatorEffectorsDNA